The True Colours of Carbon

Carbon offset projects in developing countries are one of the principal mechanisms designed to reduce greenhouse gas emissions and promote sustainable development yet have critical limitations in both areas. Here we present a framework for categorizing carbon offset projects according to four general approaches to the reduction of greenhouse gas emissions: (1) efficiency ('Brown'); innovation ('Red'), terrestrial sequestration ('Green') or sequestration in aquatic environments ('Blue'). Analysis of the 6109 CDM projects currently in the CDM "pipeline" reveals that 99% are Brown or Red, and only 1% are Green or Blue, yet Green and Blue projects typically offer a far greater range of benefits for ecosystems and society. The analysis concludes that the designers of emissions trading schemes should endorse Green and Blue offset projects as preferred forms of emissions offsetting, and that firms using offsets for compliance purposes be required to declare in public reports the colours of their offset acquisitions. Such reform will help redirect demand in carbon markets toward blue and green offset projects, increasing the sustainability outcomes of carbon offset developments

Temperature change and Baltic sprat: from observations to ecological-economic modelling

Temperature effects on Baltic sprat are many and include both direct and indirect effects. Increasing temperature is thought to increase the survival of all early life stages, resulting in increased recruitment success. We quantified the spatially resolved temperature trend for major spawning grounds and depth layers being most relevant for sprat eggs and larvae, using a three-dimensional hydrodynamic model for 1979–2005. Results confirmed an underlying positive temperature trend. Next, we tested these time-series as new explanatory variables in an existing temperature-dependent recruitment function and applied these recruitment predictions in an agestructured ecological–economic optimization model, maximizing for profit. Economic optimal solutions depended upon variability in temperature trajectories. Under climate-change scenarios, mean optimal fishing mortality and related yields and profits increased. The extent of the increase was limited by the general shape of the stock–recruitment model and the assumption of density-dependence. This highlights the need to formulate better environmentally sensitive stock recruitment models. Under the current knowledge of Baltic sprat recruitment, the tested climate-change scenarios would result in a change in management targets. However, to serve as a quantitative management advice tool, models will have to address the above-mentioned concern

Genetic Divergence across Habitats in the Widespread Coral Seriatopora hystrix and Its Associated Symbiodinium

Background: Coral reefs are hotspots of biodiversity, yet processes of diversification in these ecosystems are poorly understood. The environmental heterogeneity of coral reef environments could be an important contributor to diversification, however, evidence supporting ecological speciation in corals is sparse. Here, we present data from a widespread coral species that reveals a strong association of host and symbiont lineages with specific habitats, consistent with distinct, sympatric gene pools that are maintained through ecologically-based selection.\ud \ud Methodology/Principal Findings: Populations of a common brooding coral, Seriatopora hystrix, were sampled from three adjacent reef habitats (spanning a ~30 m depth range) at three locations on the Great Barrier Reef (n = 336). The populations were assessed for genetic structure using a combination of mitochondrial (putative control region) and nuclear (three microsatellites) markers for the coral host, and the ITS2 region of the ribosomal DNA for the algal symbionts (Symbiodinium). Our results show concordant genetic partitioning of both the coral host and its symbionts across the different habitats, independent of sampling location.\ud \ud Conclusions/Significance: This study demonstrates that coral populations and their associated symbionts can be highly structured across habitats on a single reef. Coral populations from adjacent habitats were found to be genetically isolated from each other, whereas genetic similarity was maintained across similar habitat types at different locations. The most parsimonious explanation for the observed genetic partitioning across habitats is that adaptation to the local environment has caused ecological divergence of distinct genetic groups within S. hystrix

DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation

Integrability of Lie systems through Riccati equations

Integrability conditions for Lie systems are related to reduction or transformation processes. We here analyse a geometric method to construct integrability conditions for Riccati equations following these approaches. This approach provides us with a unified geometrical viewpoint that allows us to analyse some previous works on the topic and explain new properties. Moreover, this new approach can be straightforwardly generalised to describe integrability conditions for any Lie system. Finally, we show the usefulness of our treatment in order to study the problem of the linearisability of Riccati equations.Comment: Corrected typo

Linear-Time Algorithms for Computing Maximum-Density Sequence Segments with Bioinformatics Applications

We study an abstract optimization problem arising from biomolecular sequence analysis. For a sequence A of pairs (a_i,w_i) for i = 1,..,n and w_i>0, a segment A(i,j) is a consecutive subsequence of A starting with index i and ending with index j. The width of A(i,j) is w(i,j) = sum_{i <= k <= j} w_k, and the density is (sum_{i<= k <= j} a_k)/ w(i,j). The maximum-density segment problem takes A and two values L and U as input and asks for a segment of A with the largest possible density among those of width at least L and at most U. When U is unbounded, we provide a relatively simple, O(n)-time algorithm, improving upon the O(n \log L)-time algorithm by Lin, Jiang and Chao. When both L and U are specified, there are no previous nontrivial results. We solve the problem in O(n) time if w_i=1 for all i, and more generally in O(n+n\log(U-L+1)) time when w_i>=1 for all i.Comment: 23 pages, 13 figures. A significant portion of these results appeared under the title, "Fast Algorithms for Finding Maximum-Density Segments of a Sequence with Applications to Bioinformatics," in Proceedings of the Second Workshop on Algorithms in Bioinformatics (WABI), volume 2452 of Lecture Notes in Computer Science (Springer-Verlag, Berlin), R. Guigo and D. Gusfield editors, 2002, pp. 157--17

Lie families: theory and applications

We analyze families of non-autonomous systems of first-order ordinary differential equations admitting a common time-dependent superposition rule, i.e., a time-dependent map expressing any solution of each of these systems in terms of a generic set of particular solutions of the system and some constants. We next study relations of these families, called Lie families, with the theory of Lie and quasi-Lie systems and apply our theory to provide common time-dependent superposition rules for certain Lie families.Comment: 23 pages, revised version to appear in J. Phys. A: Math. Theo

The Nondeterministic Waiting Time Algorithm: A Review

We present briefly the Nondeterministic Waiting Time algorithm. Our technique for the simulation of biochemical reaction networks has the ability to mimic the Gillespie Algorithm for some networks and solutions to ordinary differential equations for other networks, depending on the rules of the system, the kinetic rates and numbers of molecules. We provide a full description of the algorithm as well as specifics on its implementation. Some results for two well-known models are reported. We have used the algorithm to explore Fas-mediated apoptosis models in cancerous and HIV-1 infected T cells